Lecture 7 - Friday September 8 2006 Lecture 7 Announcements...

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Friday, September 8, 2006 Lecture 7 Announcements 1. Mean score for each quiz, Quiz 1A 22.6 Quiz 1B 20.6 Quiz 1C 20.7 2. Regrade policy: submit written ( WRITTEN, NOT ORAL ) argument, attached to quiz. Place in purple Re-Grade Folder at front of classroom. You will have one week after the quizzes are returned to submit a quiz for re-grading. 3. If you do not pick up your quiz today at the end of lecture, you can find your quiz at the Reserve Desk of the Bio Center, 2 nd floor of Stimson. 4. Quiz 2 on Wed 9/13 will cover lectures 4, 5, 6, 7. Policy reminder: If you missed Quiz 1 (or if you miss any quiz for any reason) you are eligible to take the make-up quiz on Wed 11/29 (which will cover the lectures from 11/13 – 11/20). 5. Meet today: Comstock B106 1:25 – 2:15PM with any interested students: How do I apply to graduate schools? What are they looking for?! 6. RasMol assignment #2: Secondary Structures. Get instruction folder from Blackboard Rasmol. Open folder, follow instructions. 7. Watch two videos! " Steric Hindrance of a Polypeptide Chain " and " Secondary Structures in Proteins " Wednesday's lecture: Characteristics of the α -helix, b-sheet, and turns Today's lecture: Alpha helix, beta sheets and turns account for a majority, about 60%, of all AAs in proteins. Nonetheless, in most proteins, some sections of the polypeptide chain do not show repeating values of φ , ψ so you don't see recognizable structure. Such "coil" or “loop” regions of proteins are certainly NOT random because they are exactly the same in every copy of that protein, but they are simply not in alpha, beta, or turn structure. These “coil” or “loop” regions must (somehow!) make all possible H-bonds, just like alpha helices and beta sheets and turns. Where we are going, where we are in this course in our study of biochemistry:
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COLLAGEN : (p. 54) 1. Found in fish scales. 2. About 30% of all our proteins are collagens: skin, tendon, bone, blood vessels, and cornea. { Collagen occurs as a triple helix, called TROPOCOLLAGEN : three helices packed together. The repeating angles are φ -60 o and ψ +140 o Every third AA is glycine, which is small enough to pack at the meeting of the 3 helices. H-bonds from the Gly N-H to the C=O across the helix axis contribute to stabilizing the helix.
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